Our research program aimed at understanding the functions of the RAG1-RAG2 protein complex in molecular detail has advanced in the past year. Starting from our crystal structure published this February, we have been able to give an explanation of the so called 12/23 rule which applies both to V(D)J recombination in lymphoid cells and to the DNA-cutting reaction of RAG1-RAG2 in vitro. This rule states that recombination and processing require a pair of different DNA sites, a so-called 12-RSS and a 23-RSS, differing in length by one turn of DNA. If the two DNA sequences are identical, there is no reaction. It was not easy to understand how a symmetrical structure could produce such an unsymmetrical result. The structure now reveals that a flexible hinge in the protein is pulled to one side by the first DNA to be bound, so that the second DNA has to have a different length in order to bind. The detailed structure has also enabled us to locate the exact amino acid altered in at least 70 human mutations that are known to cause severe combined immune deficiency (SCID) or a variant form of the same disorder known as Omenn syndrome. In many cases, the structure explains why the mutation leads to defective activity. Work is continuing on obtaining structures of different forms of the RAG1-RAG2 complex, both before and after its reaction cycle. We also completed our study of the effects of auto-ubiquitination of RAG1 on the activity of the RAG1-RAG2 protein. Ubiquitination proves to be important both for stimulating the DNA cleavage activity of RAG1-RAG2, and for a later stage of recombination in cells, at the steps that achieve the final repair and rejoining of the DNA products. This work has now been published.